Thursday, October 31, 2013

Photo: Darvin DeShazerOkay, that's not really blood. The Bleeding Tooth Fungus (Hydnellum peckii) leaks red, pink, yellow or orange fluid.Good news, the mushrooms are not poisonous, though they are considered inedible due to their bad taste. Too bad. Doesn't this look delicious?Photo: Bernypisa, 8/17/2005More on this at Environmental graffiti.

Wednesday, October 30, 2013

Judging from my Facebook wall, giraffes seem to be the rage right now. Here’s a riddle that’s a bit more meaningful than what to open first when your parents come over for early morning sandwiches: how do the different African giraffe species maintain their distinct lineages when their territories overlap?

There are three giraffe species in East Africa: Masai (Giraffa tippelskirchi), Rothschild’s (G. camelopardalis), and Reticulated (G. reticulata). While members of these different species will readily hybridize in zoos, this rarely happens in the wild. Mitochondrial DNA data suggests that the different species haven’t co-mingled for at least 200,000 years, and in some cases, over 1.5 million years. What’s been keeping them apart?

A detailed climactic analysis conducted by UCLA scientists shows that rainfall follows a predictable pattern in the region, resulting in a progression of ‘green-up’ areas. It’s this seasonal timing of rainfall that keeps the species separate. How? Each species synchronizes its reproductive cycle to a particular rainfall schedule so that its calves can take advantage of rain-lush vegetation.

When the scientists modeled where they expected to find the three giraffe species, based on monthly rainfall, it aligned extremely well with locations where giraffes were actually found.

Tuesday, October 29, 2013

Two and a half years ago, a child was born with an HIV infection that he got from his mother. While tragic, this part of the story is hardly surprising. Over 250,000 babies are born with HIV each year. However, this particular infant’s story takes a turn toward the amazing. He may be the second person ever to have been cured of AIDS.

At 30 hours old, the baby tested positive for HIV and was put on an aggressive anti-retroviral treatment (ART) regimen. His HIV titers steadily decreased until they were undetectable at 29 days, which is a typical pattern for infected individuals undergoing ART. However, when people discontinue their treatment, their HIV levels rapidly rebound. Not so with this little guy.

Based on pharmacy refill records, clinic visits and the mother’s report, the child had had no ART since the age of 18 month, and possibly none since 15 months. Yet, at least 18 months after the cessation of all treatment, the child still shows no signs of HIV infection.

The fact that this child’s HIV infection did not return suggests that the ART eliminated the reservoirs of dormant virus that usually persist despite all treatments.

To be clear, doctors prefer to use the word ‘remission’ rather than cure when talking about HIV. Like with cancer, it’s possible that the disease will return at some point. So far, for this child, remission looks as good as a cure.

The authors ruled out laboratory error as an alternate reason for the disappearance of HIV positive status since the child had had five positive tests and responded to ART in a typical fashion. For similar reasons, they discount the possibility that the HIV in the child’s bloodstream had been due not to an active infection but to maternal blood circulating through the infant.

The child also does not have any of the markers seen in the tiny subset of patients whose immune systems can naturally control HIV. The one other case of HIV remission, known as the ‘Berlin Patient’, became HIV-negative after receiving a bone marrow transplant from one of these 'super HIV suppressors'.

Our findings suggest that this child's remission is not a mere fluke but the likely result of aggressive and very early therapy that may have prevented the virus from taking a hold in the child's immune cells.

Monday, October 28, 2013

If you could observe individual bacteria, you would see that they lead a rich life of interaction with each other and their environment. Bacteria cooperate and they compete with each other. These relationships are largely driven by chemical cues in the immediate vicinity, which could be no more than a few micrometers across. Therefore, if you’re going to parse out how these microenvironments affect bacteria, including their reproduction and virility, you’ll need to be to make really tiny little test chambers for them. That’s exactly what Jodi Connell and her colleagues from the University of Texas at Austin did.

The researchers mixed bacteria with warm gelatin and a photosensitive molecule that promotes chemical cross-linking when excited. As the gelatin cools, it slowly solidifies with the bacteria suspended throughout. A carefully aimed laser results in sturdy, cross-linked microstructures around individual bacteria. In other words, the scientists made tiny cages around the bacteria.

The structures are imaged in red through confocal fluorescence, while the bacterial microcommunities are imaged in green. Credit: Jason Shear

The technique can be used to mix small numbers of bacteria from the same or different species together under different conditions. The gelatin matrix used is also highly permeable to a variety of compounds, allowing the researchers to test how the bacteria react to all sorts of molecules. Of particular interest was how normally susceptible bacteria can be sheltered from antibiotic toxicity by the presence of resistant bacteria.You can see one such experiment below:

Friday, October 25, 2013

3D printing is not only a fun, interesting way to design and make things, but it’s also good for the environment. Megan Kreiger and Joshua Pearce from Michigan Technological University have found that products made with 3D printers have a lower environment impact than the same items made using conventional manufacturing methods.

Everything from lab equipment to body parts can now be made by 3D printers. However, doing so requires energy and raw materials. Given the necessity of combating climate change, it’s important to know what the net effect would be of moving more and more manufacturing into homes and businesses.

The researchers followed the energy consumption and greenhouse emissions for every aspect of manufacturing three items (a Naef building block, a water spout and a juicer, shown above) either with a RepRap 3D printer or in a conventional factory. The analysis including everything from the extraction of the raw materials, to assembly, to shipping from overseas (which is a realistic scenario for plastic items).

The 3D printers had a smaller carbon footprint than conventional manufacturing. This was largely because 3D printed products can be made with specified fill levels (as seen below) that use considerably less material than factory-made products.

Energy usage can be decreased even more if the 3D printers are powered by solar panels or other renewable energy sources. And the total manufacturing cost goes down still more if the filament used in printing was itself recycled. For example, the authors calculate that the juicer might cost as little as four cents if printed with home-made filament, compared to at least $7 in a shop.Of course, you still have the initial cost of the 3D printer and of the filament recycler, and that’s going to cost several hundred bucks even if you make them yourself. However, the time is fast approaching when printing your own household items will be cheaper than going to the hardware store. It will also be better for the planet.

Thursday, October 24, 2013

Three words you don’t want to hear are ‘inherited herpes virus’. It’s bad enough that herpes is so contagious, but now we learn that the virus can be integrated into the genome. In other words, according to researchers led by Yan Huang of the University of Leicester, some people are conceived with herpes. To make matters worse, herpes virus can ‘escape’ from its chromosomal home and become a free agent.

There are actually lots of different human herpes viruses (HHVs). You know one common type (HHV-3) as chickenpox. Most of these viruses can lay low in the body, persisting without detection for many decades. However, the viral nucleic acids usually remain separate from those of the host. In the case of HHV-6, the researchers found that the viral DNA had become incorporated into the host cell's genome. Apparently, about 0.8% of the British population were HHV-6 carriers.

More specifically, the virus integrates into the telomeres at the ends of chromosomes. This region is particularly unstable and made more so by the addition of the viral DNA. This makes it more likely that the viral DNA will be shed from the ends of the chromosomes. Once this happens, it’s possible for the virus to infect new cells. These data suggest that a person could be born with HHV-6 already present within the DNA he inherited from a parent, and that the embedded virus could at any point cause a full blown infection. While this isn’t good news for anyone, it’s especially problematic for immuno-compromised blood and organ recipients. Currently, donation programs screen blood products for infectious agents but not for gene sequences that might become reactivated at any moment.Yan Huang, Alberto Hidalgo-Bravo, Enjie Zhang, Victoria E. Cotton, Aaron Mendez-Bermudez, Gunjan Wig, Zahara Medina-Calzada, Rita Neumann, Alec J. Jeffreys1, Bruce Winney2, James F. Wilson3, Duncan A. Clark, Martin J. Dyer, & Nicola J. Royle (2013). Human telomeres that carry an integrated copy of human herpesvirus 6 are often short and unstable, facilitating release of the viral genome from the chromosome Nucleic Acids Research DOI: 10.1093/nar/gkt840.

Wednesday, October 23, 2013

Getting a tattoo may not be the wisest course of action if you plan to one day look for a job. That's the conclusion that Andrew Timming delivered at the British Sociological Association conference on work, employment and society:

Most respondents agreed that visible tattoos are a stigma...Respondents expressed concern that visibly tattooed workers may be perceived by customers to be 'abhorrent', 'repugnant', 'unsavoury' and 'untidy'.

Of course, if your tattoo displays how much you love your work, you might get the opposite result. What neuroscientist wouldn't hire this guy as a postdoc?

Gabriel Pato, a Brazilian biologist, carries on his body the principle that the brain is a network. Neurons send signals to thousands of other neurons, and it is the number and the strength of those connections from which our thoughts emerge.Credit: “Science Ink” by Carl Zimmer/Sterling Publishing

Tuesday, October 22, 2013

Concussions (aka mild traumatic brain injuries) are the result of the brain slamming against the inside of the skull. This can be caused either by rapid deceleration of the entire body or by direct impact to the head. Either way, the brain has a bruise that must heal. Opinions differ on how long that recovery takes, and on whether some groups, particularly children, are more vulnerable during the healing process. To answer this question, scientists from the Vanderbilt University School of Medicine compared ninety-two 13 to 16 year-old kids with the same number of 18 to 22 year-olds who had all suffered a sports related concussion. Each participant was evaluated for a number of different symptoms (headache, nausea, irritability, etc) and for how long it took for those symptoms to completely resolve.

Immediately after the head trauma, there was no difference in reported symptoms between the two groups. Younger and older people experienced the same number and severity of symptoms. By thirty days post concussion, nearly everyone (96% of the younger participants and 97% of older ones) had returned to normal. On average, the 13 to 16 year-olds took slightly longer than 18 to 22 year-olds to lose all their concussion symptoms (7 days rather than 6 days) but this was not statistically significant. In other words, there really wasn't much difference between young teens and young adults.

These data contradict other studies that show that concussions are more dangerous and long-lasting for younger people. I wonder if the differences between the groups discussed here would have become significant in a larger study group. In any case, coaches and parents should use extreme caution before sending young athletes back into play, especially during the first week.Young M. Lee, Mitchell J. Odom, Scott L. Zuckerman, Gary S. Solomon,, & Allen K. Sills (2013). Does age affect symptom recovery after sports-related concussion? A study of high school and college athletes
Clinical article Journal of Neurosurgery DOI: 10.3171/2013.7.PEDS12572.

Monday, October 21, 2013

What’s a bird to do if his flight-approved, aerodynamic tail isn’t showy enough to attract the ladies? Have two tails of course. Anyway, that seems to be how the Early Cretaceous bird Jeholornis solved this problem. Scientists led by Jingmai O’Connor of the Chinese Academy of Sciences discovered that Jeholornis had two functional tails.

Before I continue, I want to make one thing clear. We’re not talking about two separate strings of vertebrae. If you remove all the feathers, Jeholornis had a normal-looking skeleton with a single long vertebral tail. However, once you put the feathers back on, you get two distinct tufts of feathers at each end of that vertebral trail that most likely served very different purposes.

In modern birds, the last few vertebrae are fused into a solid structure called the ‘pygostyle’. The flight feathers of a bird’s tail (rectrices) are attached to the pygostyle. Jeholornis had a broad fan of feathers at the base of its backbone, similar to that seen on modern birds, but unlike all known birds, those feathers are not attached to a pygostyle. The authors suspect that this may be a feature that is unique to this species. This first ‘tail’ no doubt assisted the animal in flight.

The second tail is composed of a feathery frond at the end of the vertebral column. This showy spread of feathers might not have hindered the bird in flight, but it was probably primarily ornamental. The researchers do not know whether it was present in both sexes or only one.

At first, I thought it was slightly misleading to say thatJeholornis had two tails, rather than a single tail containing two distinct features. However, these two parts of its anatomy not only served different functions, but were also attached to the body in different ways. So, I’m sticking with my title.

Jingmai O’Connor, Xiaoli Wang, Corwin Sullivan, Xiaoting Zheng, Pablo Tubaro, Xiaomei Zhang, & Zhonghe Zhou (2013). Unique caudal plumage of Jeholornis and complex tail evolution in early birds Proceedings of the National Academy of Sciences of the United States of America DOI: 10.1073/pnas.1316979110.

Friday, October 18, 2013

Pain researchers who are looking for new drugs to treat and manage pain often look to nature for new compounds. Yesterday, I wrote about a promising new pain medication found in centipede venom. Once we find a useful natural product, we attempt to synthesize it in the lab. However, here’s a case where the opposite happened. Scientists had first created a synthetic pain-killer called tramadol (a modification of morphine) and later discovered that this same compound already exists in the wild.

In sub-Saharan Africa, there’s a tree (the African pincushion tree Nauclea latifolia) that the local people have used for generations to treat a variety of illnesses. The root bark of this plant is traditionally used to provide pain relief. Upon further investigation, an international team of scientists were able to isolate the molecules responsible for this effect. To their surprise, it was identical to tramadol.

The analgesic tramadol has been isolated from the root bark of N. latifolia, an African medical plant. This finding is a rare example of a common synthetic drug that occurs at considerable concentrations in nature. Cl purple, N blue, O red.doi: 10.1002/anie.201305697.The N. latifolia version of tramadol was not only just as effective as the synthetic version in relieving pain (tested on poor little mice), but was also found in considerable concentrations (up to 4%) within the root bark. Taken together, it's no wonder the plant has long been used as a medicine by indigenous peoples.

The authors point out that there are at least nine other species of Nauclea in Africa that might also contain useful and intriguing compounds. I'd say they are definitely worth a thorough investigation, especially considering that the interesting compound in N. latifolia was found only in the root bark and not in any other parts of the plant.Boumendjel, A., Sotoing Taïwe, G., Ngo Bum, E., Chabrol, T., Beney, C., Sinniger, V., Haudecoeur, R., Marcourt, L., Challal, S., Ferreira Queiroz, E., Souard, F., Le Borgne, M., Lomberget, T., Depaulis, A., Lavaud, C., Robins, R., Wolfender, J.-L., Bonaz, B. and De Waard, M. (2013), Occurrence of the Synthetic Analgesic Tramadol in an African Medicinal Plant . Angew. Chem. Int. Ed.. doi: 10.1002/anie.201305697.

Thursday, October 17, 2013

If you suffer from chronic pain, there’s a good chance that your voltage-gated sodium channels are to blame. Humans have nine types of these channels, but one in particular, NaV1.7, is responsible for the sensation of some types of severe, episodic pain. I’ve explained the workings of NaV1.7 in a previous post, so go there for some background.

This means that NaV1.7 would make an excellent target for an analgesic drug. That’s certainly what researchers led by Shilong Yang of the Chinese Academy of Sciences thought, and they have just the candidate: a protein found in centipede venom.

Scolopendra subspinipes mutilans

Photo by KENPEI, Osaka, Japan, 6/28/09.

It turns out that venom of the Chinese red-headed centipede (Scolopendra subspinipes mutilans) includes a peptide (Ssm6a) that can block NaV1.7 sodium channels. Remember, as long as the channels are closed, you can’t feel any pain. The scientists were able to reversibly block the NaV1.7 channels in mice and in human cells grown in culture. More importantly, Ssm6a offered the mice substantial pain relief, as measured by the number of times some unfortunate mice licked their aching feet. In fact, Ssm6a was significantly more effective than morphine.

The effects of Ssm6a lasted several hours, probably until the peptide was cleared by liver and kidneys. Unlike other NaV1.7 blockers, Ssm6a has little or no effect on our other eight sodium channels, making it particularly appealing as a pain drug. Previously tried drugs were less specific, and thus could not be safely administered because blocking the other sodium channels can lead to paralysis, seizure or death.

Obviously there’s a long way to go between a mouse licking its paws and a new drug on the shelf. Still, the researchers are hopeful that Ssm6a will one day help to alleviate chronic, persistent pain.

Wednesday, October 16, 2013

Okay, normally, aging isn't that much fun. It can be amazing though, if it's captured from early childhood to old age by filmmaker Anthony Cerniello. After you watch it, you'll want to read how he did it at io9.

Tuesday, October 15, 2013

The second name probably rings a bell. Ever hear of the Higgs Boson? Here's a hint: it's an elementary particle that was not named by Peter Higgs.The Nobel committee's reasoning:"For the theoretical discovery of a mechanism that contributes to our understanding of the origin of mass of subatomic particles, and which recently was confirmed through the discovery of the predicted fundamental particle, by the ATLAS and CMS experiments at CERN's Large Hadron Collider."If you didn't find that clear, perhaps this will help:Or how about this. Or this. Or maybe this.In Chemistry:

"For the development of multiscale models for complex chemical systems."Translation: they created software programs to model complex molecular interactions.
In Physiology or Medicine: James E. Rothman,Randy W. Schekman and Thomas C. Südhof"For their discoveries of machinery regulating vesicle traffic, a major transport system in our cells."There must be tight control over when molecules enter or leave a cell and where within the cell those molecules are located. We now have a better understanding of how this works.Take a look:

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.